CipaQNetCalculator.cpp

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*/

// Chaste includes
#include "CellProperties.hpp"
#include "Warnings.hpp"

// ApPredict includes
#include "CipaQNetCalculator.hpp"
#include "ohara_rudy_cipa_v1_2017Cvode.hpp"

CipaQNetCalculator::CipaQNetCalculator(boost::shared_ptr<AbstractCvodeCell> pModel)
        : mpModel(pModel)
{
    if (!boost::dynamic_pointer_cast<Cellohara_rudy_cipa_v1_2017FromCellMLCvode>(mpModel))
    {
        EXCEPTION("Model used in constructor of CipaQNetCalculator needs to be an Ohara-Rudy-CiPA-v1 model.");
    }

    mpStimulus = boost::static_pointer_cast<RegularStimulus>(mpModel->GetStimulusFunction());
    if (mpStimulus->GetPeriod() != 2000)
    {
        WARNING("qNet should be calculated at 0.5Hz (pacing cycle length of 2000ms), your stimulus is set to " << mpStimulus->GetPeriod() << "ms.");
    }
}

double CipaQNetCalculator::ComputeQNet()
{
    const double maximum_time_step = mpStimulus->GetDuration();
    const double sampling_interval = 0.01; //ms
    OdeSolution detailed_solution = mpModel->Solve(0, mpStimulus->GetPeriod(), maximum_time_step, sampling_interval);

    std::vector<double> times = detailed_solution.rGetTimes();
    std::vector<double> voltages = detailed_solution.GetAnyVariable("membrane_voltage");

    // Analyse trace to check there is actually an AP.
    CellProperties cell_properties(voltages, times, 0 /* mV threshold */);
    try
    {
        cell_properties.GetTimesAtMaxUpstrokeVelocity();
        cell_properties.GetAllActionPotentialDurations(30);
        cell_properties.GetAllActionPotentialDurations(90);
    }
    catch (Exception& e)
    {
        if (e.GetShortMessage() == "AP did not occur, never descended past threshold voltage."
            || e.GetShortMessage() == "No full action potential was recorded")
        {
            std::cout << "Action potential de/repolarisation failure, logging -DBL_MAX for the qNet calculation" << std::endl;
            return -DBL_MAX;
        }
        else
        {
            throw(e);
        }
    }

    detailed_solution.CalculateDerivedQuantitiesAndParameters(mpModel.get());

    // Inet = ICaL + INaL + IKr + IKs + IK1 + Ito
    std::vector<double> i_cal = detailed_solution.GetAnyVariable("membrane_L_type_calcium_current");
    std::vector<double> i_nal = detailed_solution.GetAnyVariable("membrane_persistent_sodium_current");
    std::vector<double> i_kr = detailed_solution.GetAnyVariable("membrane_rapid_delayed_rectifier_potassium_current");
    std::vector<double> i_ks = detailed_solution.GetAnyVariable("membrane_slow_delayed_rectifier_potassium_current");
    std::vector<double> i_k1 = detailed_solution.GetAnyVariable("membrane_inward_rectifier_potassium_current");
    std::vector<double> i_to = detailed_solution.GetAnyVariable("membrane_transient_outward_current");
    std::vector<double> i_net(i_cal.size());

    // assume equal spacing and convert from milliseconds to seconds.
    const double timestep_in_seconds = (detailed_solution.rGetTimes()[1] - detailed_solution.rGetTimes()[0]) / 1000.0;

    // Integrate over the whole AP.
    double q_net = 0.0; // Charge
    i_net[0] = i_cal[0] + i_nal[0] + i_kr[0] + i_ks[0] + i_k1[0] + i_to[0]; // Current

    for (unsigned i = 1u; i < i_cal.size(); i++)
    {
        i_net[i] = i_cal[i] + i_nal[i] + i_kr[i] + i_ks[i] + i_k1[i] + i_to[i]; // uA/uF

        // Hack in a trapezium rule for the integral, should be enough accuracy with this time resolution.
        q_net += timestep_in_seconds * 0.5 * (i_net[i] + i_net[i - 1]); // Coulomb is Amps * seconds (rather than milliseconds), so integral in uC/uF.
    }

    return q_net;
}